Addressing heterogeneity of individual blood cancers: the need for single cell analysis

Single-Cell Sequencing: Ariadne’s Thread in the Maze of Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a haematological neoplasm resulting from the accumulation of genetic and epigenetic alterations. Patients’ prognoses vary with AML genetic heterogeneity, which hampers successful treatments. Single-cell approaches have provided new insights of the clonal architecture of AML, revealing the mutational history from diagnosis, during treatment and to relapse. In this review, we imagine single-cell technologies as the Ariadne’s thread that will guide us out of the AML maze, provide a precise identikit of the leukemic cell at single-cell resolution and explore genomic, transcriptomic, epigenetic and proteomic levels.

Clinical lipidomics in understanding of lung cancer: Opportunity and challenge

Disordered lipid metabolisms have been evidenced in lung cancer as well as its subtypes. Lipidomics with in-depth mining is considered as a critical member of the multiple omics family and a lipid-specific tool to understand disease-associated lipid metabolism and disease-specific dysfunctions of lipid species, discover biomarkers and targets for monitoring therapeutic strategies, and provide insights into lipid profiling and pathophysiological mechanisms in lung cancer. The present review describes the characters and patterns of lipidomic profiles in patients with different lung cancer subtypes, important values of comprehensive lipidomic profiles in understanding of lung cancer heterogeneity, urgent needs of standardized methodologies, potential mechanisms by lipid-associated enzymes and proteins, and the importance of integration between clinical phenomes and lipidomic profiles. The characteristics of lipidomic profiles in different lung cancer subtypes are extremely varied among study designs, objects, methods, and analyses. Preliminary data from recent studies demonstrate the specificity of lipidomic profiles specific for lung cancer stage, severity, subtype, and response to drugs. The heterogeneity of lipidomic profiles and lipid metabolism may be part of systems heterogeneity in lung cancer and be responsible for the development of drug resistance, although there are needs for direct evidence to show the existence of intra- or inter-lung cancer heterogeneity of lipidomic profiles. With an increasing understanding of expression profiles of genes and proteins, lipidomic profiles should be associated with activities of enzymes and proteins involved in the processes of lipid metabolism, which can be profiled with genomics and proteomics, and to provide the opportunity for the integration of lipidomic profiles with gene and protein expression profiles. The concept of clinical trans-omics should be emphasized to integrate data of lipidomics with clinical phenomics to identify disease-specific and phenome-specific biomarkers and targets, although there are still a large number of challenges to be overcome in the integration between clinical phenomes and lipidomic profiles.

Roles of cohesin in chromosome architecture and gene expression

Cohesin-mediated chromatin organization plays an important role in formation and stabilization of chromosome architecture and gene regulation. Mechanisms by which cohesin shapes chromosome and regulates gene expression remain unclear. The present article overviews biological characters and functions of cohesin and core subunits and explores roles of regulatory factors (e.g. Pds5, Wapl, and Eco1) in dynamic behaviors of cohesin. Cohesin interacts with CCCTC binding factor (CTCF) and other factors to maintain and stabilize multi-dimensional organizations of topological loops and distances between sites during cell segmentation. We also describe functional roles of cohesin in cell cycle by entrapping sister chromatids to form embrace and handcuff models, loading onto chromatin, establishing cohesion function, and regulating removal of cohesin and associated factors from the chromosome arm through prophase pathway or at onset of anaphase. It is questioned whether those factors associated with cohesin-regulated processes can be identified as biology- or disease-specific biomarkers and druggable targets to dynamically monitor changes during phasing, staging, progressing, and responding of diseases. It is also expected to explore heterogenetic roles of cohesin between single cells and regulatory roles of cohesin in trans-omic profiles and functions. Further understanding of cohesin functions will be beneficial to improve diagnosis and treatment of cohesinopathies.

A tour of 3D genome with a focus on CTCF

The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.

Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis

In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.

Is Pooled CRISPR-Screening the Dawn of a New Era for Functional Genomics

Functional genomics aims to develop an in-depth understanding of how specific gene dysfunctions are related to diseases. A common method for investigating the genome and its complex functions is via perturbation of the interactions between the DNA, RNA and their protein respective protein derivatives. Commonly, arrayed and pooled genetic screens are utilized to achieve this and in recent years have been fundamental in achieving the current level of understanding for gene dysfunctions. However, they are limited in specific aspects which scientists have attempted to address. Clustered regularly palindromic repeats (CRISPR)-based methods for genetic screens have in recent years become more prevalent but crucially shared similar properties to previous methods and failing to provide a distinct advantage over previous methods. CROP-seq, Perturb-seq, and CRISPR-seq have combined CRISPR and single-cell RNA-sequencing (scRNA-seq) and is the newest addition to the geneticist's arsenal, providing scientists with methods to edit DNA with improved speed, accuracy, and efficiency which could usher us into a new era of study methods for functional genomics. We briefly overview the CRISPR-Cas9 systems, the evolution of genetic screening in recent years, and evaluate and discuss the significance of CROP-seq, Perturb-seq, and CRISPR-seq.

Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq

The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.

CRISPR Technology for Breast Cancer: Diagnostics, Modeling, and Therapy

Molecularly, breast cancer represents a highly heterogenous family of neoplastic disorders, with substantial interpatient variations regarding genetic mutations, cell composition, transcriptional profiles, and treatment response. Consequently, there is an increasing demand for alternative diagnostic approaches aimed at the molecular annotation of the disease on a patient-by-patient basis and the design of more personalized treatments. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) technology enables the development of such novel approaches. For instance, in diagnostics, the use of the RNA-specific C2c2 system allows ultrasensitive nucleic acid detection and could be used to characterize the mutational repertoire and transcriptional breast cancer signatures. In disease modeling, CRISPR/Cas9 technology can be applied to selectively engineer oncogenes and tumor-suppressor genes involved in disease pathogenesis. In treatment, CRISPR/Cas9 can be used to develop gene-therapy, while its catalytically-dead variant (dCas9) can be applied to reprogram the epigenetic landscape of malignant cells. As immunotherapy becomes increasingly prominent in cancer treatment, CRISPR/Cas9 can engineer the immune cells to redirect them against cancer cells and potentiate antitumor immune responses. In this review, CRISPR strategies for the advancement of breast cancer diagnostics, modeling, and treatment are highlighted, culminating in a perspective on developing a precision medicine-based approach against breast cancer.

The advances in CRISPR technology and 3D genome

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is a prokaryotic immune system that used to resist foreign genetic factors. It rapidly becomes the hot technology in life sciences and is applies for genome editing to solve the problem of genome-derived diseases. Using CRISPR/Cas technique, the biological DNA sequence can be repaired, cut, replaced, or added. It can effectively change the human stem cells and is expected to achieve results in the treatment. Compared with ZFN and TALEN genome editing techniques, CRISPR is more effective, accurate, and convenient. The application of CRISPR technique in three dimensional (3D) genome structure makes us understand the relationship between linear DNA sequence and 3D chromatin structure. Utilizing CRISPR/Cas9 genome editing to reverse or delete CTCF binding sites, to recognize changes of topological isomerism of the genome and interactions between chromatin loops. The purpose of this review is to introduce the characteristics and classification of the current CRISPR/Cas system, multiple functions, and potential therapeutic uses, as well as to outline the effect of the technique on chromatin loops by changing CTCF sites in 3D genomes. We will also briefly describe the importance of ethical dilemmas to be faced in CRISPR applications and provide a perspective for potential CRISPR considerations.

Roles of NIPBL in maintenance of genome stability

A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-binding factor (CTCF) or cohesin complex component. The present article overviews the critical and regulatory roles of NIBPL in cohesion loading on chromotin and in gene expression and transcriptional signaling. We explore molecular mechanisms by which NIPBL recruits endogenous histone deacetylase (HDAC) to induce histone deacetylation and influence multi-dimensions of genome, through which NIPBL "hop" movement in chromatin regulates gene expression and alters genome folding. NIPBL regulates the process of CTCF and cohesion into chromatin loops and topologically associated domains, binding of cohesion and H3K4mes3 through interaction among promoters and enhancers. HP1 recruits NIPBL to DNA damage site through RNF8/RNF168 ubiquitylation pathway. NIPBL contributes to regulation of genome-controlled gene expression through the influence of cohesin in chromosome structure. NIPBL interacts with cohesin and then increases transcriptional activities of REC8 promoter, leading to up-regulation of gene expression. NIPBL movement among chromosomal loops regulates gene expression through dynamic alterations of genome organization. Thus, we expect a new and deep insight to understand dynamics of chromosome and explore potential strategies of therapiesc on basis of NIPBL.

Roles of Single Cell Systems Biomedicine in Lung Diseases

Single cell sequencing is important to detect the gene heterogeneity between cells, as the part of single-cell systems biology which combines computational science, mathematical modelling and high-throughput technologies with biological function and organization in the cell. We initially arise the question how to integrate the outcomes of single-cell systems biology with clinical phenotype, interpret alterations of single-cell gene sequencing and function in patient response to therapies, and understand the significance of single-cell systems biology in the discovery and development of new molecular diagnostics and therapeutics. The present review furthermore focuses the significance of singe cell systems biology in respiratory diseases and calls the special attention from scientists who are working on single cell systems biology to improve the diagnosis and therapy for patients with lung diseases.

Can the Single Cell Make Biomedicine Different?

The single-cell as the basic unit of biological organs and tissues has recently been considered an important window to furthermore understand molecular mechanisms of organ function and biology. The current issue with a special focus on single cell biomedicine is the first effort to collect the evidence of disease-associated single cell research, define the significance of single cell biomedicine in the pathogenesis of diseases, value the correlation of single cell gene sequencing with disease-specific biomarkers, and monitor the dynamics of RNA processes and responses to microenvironmental changes and drug resistances.

Regulatory Roles of Mitochondrial Ribosome in Lung Diseases and Single Cell Biology

The mitochondria have the most vital processes in eukaryotic cells to produce ATP composed of polypeptides that are produced via ribosomes, as oxidative phosphorylation. Initially, studies regarding human mitochondrial ribosomes were performed in the model system, bovine mitochondrial ribosome, to investigate how ribosomes are biosynthesized and evolved as well as what their structure and function are. Advances in X-ray crystallography have led to dramatic progresses in structural studies of the ribosome. In recent years, there has been a growing interest in the properties of the mitochondrial ribosome. Although one of its main functions is the production of ATP, it was also linked to multiple diseases. A key area that remains unexplored and requires investigation and exploration is how mitochondrial ribosomal RNA (mt-rRNA) variations can affect the mitochondrial ribosomes in developing disease. This review summarizes the structure, elements, functions, and regulatory roles in associated diseases. With the continuous development of technology, studies on the mechanism of mitochondrial ribosome related diseases are crucial, in order to identify methods of prevention and treatment of these disorders.

Mitochondrial DNA in Telocytes

Telocyte (TC) is a new identified interstitial cell type with a small nuclear and one or several long and thin prolongations with enlargements on them. They were found in many mammals including humans, mouse, rats, dogs, and monkeys and play vital roles in many physiological and pathological conditions. The ultrastructure of mitochondria was observed in TCs, and the alterations were found in TCs from inflammatory ureter tissue. MtDNA is associated with mitochondria normal functions and involved in physiological and pathological processes. However, mitochondria and mtDNA in TCs were not investigated deeply. This review will introduce the origin, distribution, morphology, and functions of TCs and the distribution and functions of TC mitochondria in order to improve a better understanding of the potential functions of mtDNA in TCs.